AF16xHK104cross | Cross object for AF16xHK104 C. brggsae RIAILs |
AF16xHK104markers | Marker/position lookup table for AF16xHK104 RIAILs |
AllCBfosmids | Dataframe of all CB4856 fosmids in the Andersen Lab |
AllCBfosmids_pacbio | Dataframe of all CB4856 fosmids in the Andersen Lab -... |
AllN2fosmids | Dataframe of all N2 fosmids in the Andersen Lab |
annotate_lods | Annotate LOD peaks with variance explained, effect size, and... |
calc_mediation | Calculate mediation scores between phenotype and gene... |
checkeQTLintervals | Find expression QTL from the Rockman dataset within a... |
count_strains_per_trait | Count number of strains with data for each phenotype from... |
effectplot | Plot effect size by marker |
eQTLpeaks | Dataframe of all eQTL peak location information from Matt... |
eqtlpheno | Expression phenotypes from Rockman 2010 paper, reanalyzed for... |
extract_genotype | Extract genotype matrix from cross structure and recode as... |
extract_scaled_phenotype | Extract phenotype matrix from cross object, mean center and... |
findCBfosmids | Find CB4856 fosmids that tile across a given interval |
findindels | Find indels to generate primers |
findN2fosmids | Find N2 fosmids that tile across a given interval |
FindRIAILsforNILs | Find RIAILs for generating NILs to isolate a genomic region |
fsearch | Map all of the traits in a given cross object with forward... |
indels | Dataframe of indels between N2 and CB4856 |
load_cross_obj | Load Cross Obj |
lodplot | Plot all lod scores for a forward search mapping by iteration |
mapformat | Get the LOD value for each marker based on the correlation... |
maxlodplot | Plot max lod scores for a forward search mapping |
mergepheno | Merge the cross object and the phenotype data frame using a... |
N2xCB4856cross | Cross object for N2xCB4856 RIAILs |
N2xCB4856cross_full | Whole genome cross object for N2xCB4856 RIAILs |
N2xCB4856markers | Marker/position lookup table for N2xCB4856 RIAILs |
N2xLSJ2cross | Cross object for N2xLSJ2 RIAILs |
N2xLSJ2markers | Marker/position lookup table for N2xLSJ2 RIAILs |
probe_info | Dataframe of GO terms, descriptions, and other information... |
pxgplot | Plot the phenotype by genotype split at each peak marker in a... |
pxgplot_par | Plot the phenotype by genotype split at each peak marker in a... |
RIAILgenotypes | Genotypes of RIAILs at each of the 1454 markers |
RIAILmarkerconversion | Marker conversions for each of the 1454 markers used in... |
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